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Stockholms högskola was founded in 1878. The first professorship was in Mathematics. In 1881, a 29 year old Norwegian geologist, Waldemar Christofer Brögger, became the second professor at Stockholms högskola. His professorship was in Geology and Mineralogy and he founded the Department of Geology and Mineralogy.

Both the title of his professorship and the name of the Department are often quoted in the reverse order: Mineralogy and Geology. In his letterheads, Brögger himself often referred to the Department of Mineralogy. However, Stockholm högskolas registry states clearly (translated from Swedish): "Brøgger, Waldemar Christofer [...] Professor of Geology and Mineralogy at Stockholms högskola [...]; founded the Department of Geology and Mineralogy […] in the autumn of 1881."

In a document about research in the biological and geological sciences at Stockholms universitet from 1972, Ivar Hessland described Brögger as follows (translated from Swedish): "From nothing and in a short time, he created, in Stockholm, a fresh and modern centre for research and education, to which young geologists from all of the Nordic countries gathered. Among these are many of the key figures in Nordic geology." Frans Erik Wickman expressed a similar view, highlighting Brögger’s nine years in Stockholm as "A seminal period of Nordic geology" (Bulletin of the Geological Society of Finland, v. 58, 1986).

Waldemar Christofer Brögger remained in Stockholm until 1890, when he was offered a professorship at the University of Kristiana (Oslo). In 1890, he expressed his longing to return to Norway in 1890 (translated from Norwegian) as follows: "Here, I cannot bear to stay forever; I miss home." Much later, in a letter to Percy Quensel, written in 1934, he states (translated from Norwegian): "I always remember my Stockholm years as my happiest years." (Geir Hestmark: "Vitenskap og nasjon, Waldemar Christopher Brøgger 1851–1905", Aschehoug, 1999).

For economic reasons, Brögger's Chair was not filled during the period 1890–1895. The geological disciplines were nevertheless carried forwards by Arvid G. Högbom who was installed as professor in 1896. During the same year, Högbom moved to Uppsala, where he held a professorship until 1922. In Stockholm, Högbom’s successor, from 1897 to 1924, was Gerard De Geer. He was also the Vice Chancellor of Stockholms högskola from 1902 to 1910. Two of the five lecture theatres in the Geoscience buildings are named after Högbom and De Geer.

The disciplines Geology and Mineralogy were undivided until 1909. Helge Bäckström was installed as Professor of Mineralogy and Petrography in 1908. Shortly thereafter, in 1909, under Bäckström’s leadership, the Department of Mineralogy separated from the Department of Geology and Mineralogy and under the leadership of Gerard De Geer, the Department of Geology was formed.

De Geer instigated the research training program Geology. His successor for a short period (1925–1926) was Johan Gunnar Andersson ("China-Gunnar"), before Lennart von Post took over as program leader for Geology beginning in 1929 and until his death in January 1951. Collectively and over a period of more than half a century (1897–1951) De Geer and von Post created a department which almost exclusively focused on Quaternary Geology.

The research training program Geology was renamed General and Historical Geology when Lennart von Post’s successor, Ivar Hessland, was installed as professor in 1953. Quaternary Geology was initially encompassed within this program, but already in 1954, Hessland had established Quaternary Geology (with an applied focus) as a separate research program with its own premises. Carl-Gösta Wenner was the first leader of this program.

Ivar Hessland established a focus on Marine Geology within the program General and Historical Geology. This new focus encompassed the following research areas: marine micropaleontology, biostratigraphy, marine geophysics, lithostratigraphy, marine sedimentology and sediment geochemistry. These areas remain vital parts of the Department’s research profile today.

General and Historical Geology switched focus towards Northern Europe’s continental bedrock and impact structures when Maurits Lindström was installed as professor in 1984. The focus of this program returned to Marine Geology when Jan Backman was installed as professor in 1997, with his interest for ocean drilling and paleoceanography. The name of this program was changed to Marine Geology in 2010 to reflect this profile, which has its origins in 1953. Jan Backman is probably the last of this lineage of professors which can be traced back to Waldemar Christofer Brögger, Stockholm högskolas second professor.

With Barbara Wohlfarth joining the Department in 2007, the Marine Geology program was broadened so as to include lacustrine environments.